RPB1_SCHPO
ID RPB1_SCHPO Reviewed; 1752 AA.
AC P36594;
DT 01-JUN-1994, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-1994, sequence version 1.
DT 03-AUG-2022, entry version 173.
DE RecName: Full=DNA-directed RNA polymerase II subunit rpb1;
DE Short=RNA polymerase II subunit 1;
DE Short=RNA polymerase II subunit B1;
DE EC=2.7.7.6;
DE AltName: Full=DNA-directed RNA polymerase III largest subunit;
GN Name=rpb1; ORFNames=SPBC28F2.12;
OS Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina;
OC Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae;
OC Schizosaccharomyces.
OX NCBI_TaxID=284812;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=972 / ATCC 24843;
RX PubMed=2011520; DOI=10.1093/nar/19.3.461;
RA Azuma Y., Yarnagishi M., Ueshima R., Ishihama A.;
RT "Cloning and sequence determination of the Schizosaccharomyces pombe rpb1
RT gene encoding the largest subunit of RNA polymerase II.";
RL Nucleic Acids Res. 19:461-468(1991).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=972 / ATCC 24843;
RX PubMed=11859360; DOI=10.1038/nature724;
RA Wood V., Gwilliam R., Rajandream M.A., Lyne M.H., Lyne R., Stewart A.,
RA Sgouros J.G., Peat N., Hayles J., Baker S.G., Basham D., Bowman S.,
RA Brooks K., Brown D., Brown S., Chillingworth T., Churcher C.M., Collins M.,
RA Connor R., Cronin A., Davis P., Feltwell T., Fraser A., Gentles S.,
RA Goble A., Hamlin N., Harris D.E., Hidalgo J., Hodgson G., Holroyd S.,
RA Hornsby T., Howarth S., Huckle E.J., Hunt S., Jagels K., James K.D.,
RA Jones L., Jones M., Leather S., McDonald S., McLean J., Mooney P.,
RA Moule S., Mungall K.L., Murphy L.D., Niblett D., Odell C., Oliver K.,
RA O'Neil S., Pearson D., Quail M.A., Rabbinowitsch E., Rutherford K.M.,
RA Rutter S., Saunders D., Seeger K., Sharp S., Skelton J., Simmonds M.N.,
RA Squares R., Squares S., Stevens K., Taylor K., Taylor R.G., Tivey A.,
RA Walsh S.V., Warren T., Whitehead S., Woodward J.R., Volckaert G., Aert R.,
RA Robben J., Grymonprez B., Weltjens I., Vanstreels E., Rieger M.,
RA Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Duesterhoeft A.,
RA Fritzc C., Holzer E., Moestl D., Hilbert H., Borzym K., Langer I., Beck A.,
RA Lehrach H., Reinhardt R., Pohl T.M., Eger P., Zimmermann W., Wedler H.,
RA Wambutt R., Purnelle B., Goffeau A., Cadieu E., Dreano S., Gloux S.,
RA Lelaure V., Mottier S., Galibert F., Aves S.J., Xiang Z., Hunt C.,
RA Moore K., Hurst S.M., Lucas M., Rochet M., Gaillardin C., Tallada V.A.,
RA Garzon A., Thode G., Daga R.R., Cruzado L., Jimenez J., Sanchez M.,
RA del Rey F., Benito J., Dominguez A., Revuelta J.L., Moreno S.,
RA Armstrong J., Forsburg S.L., Cerutti L., Lowe T., McCombie W.R.,
RA Paulsen I., Potashkin J., Shpakovski G.V., Ussery D., Barrell B.G.,
RA Nurse P.;
RT "The genome sequence of Schizosaccharomyces pombe.";
RL Nature 415:871-880(2002).
RN [3]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1489; SER-1499; SER-1506;
RP SER-1529 AND TYR-1531, AND IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=18257517; DOI=10.1021/pr7006335;
RA Wilson-Grady J.T., Villen J., Gygi S.P.;
RT "Phosphoproteome analysis of fission yeast.";
RL J. Proteome Res. 7:1088-1097(2008).
CC -!- FUNCTION: DNA-dependent RNA polymerase catalyzes the transcription of
CC DNA into RNA using the four ribonucleoside triphosphates as substrates.
CC Largest and catalytic component of RNA polymerase II which synthesizes
CC mRNA precursors and many functional non-coding RNAs. Forms the
CC polymerase active center together with the second largest subunit. Pol
CC II is the central component of the basal RNA polymerase II
CC transcription machinery. It is composed of mobile elements that move
CC relative to each other. RPB1 is part of the core element with the
CC central large cleft, the clamp element that moves to open and close the
CC cleft and the jaws that are thought to grab the incoming DNA template.
CC At the start of transcription, a single-stranded DNA template strand of
CC the promoter is positioned within the central active site cleft of Pol
CC II. A bridging helix emanates from RPB1 and crosses the cleft near the
CC catalytic site and is thought to promote translocation of Pol II by
CC acting as a ratchet that moves the RNA-DNA hybrid through the active
CC site by switching from straight to bent conformations at each step of
CC nucleotide addition. During transcription elongation, Pol II moves on
CC the template as the transcript elongates. Elongation is influenced by
CC the phosphorylation status of the C-terminal domain (CTD) of Pol II
CC largest subunit (RPB1), which serves as a platform for assembly of
CC factors that regulate transcription initiation, elongation, termination
CC and mRNA processing (By similarity). {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate +
CC RNA(n+1); Xref=Rhea:RHEA:21248, Rhea:RHEA-COMP:14527, Rhea:RHEA-
CC COMP:17342, ChEBI:CHEBI:33019, ChEBI:CHEBI:61557, ChEBI:CHEBI:140395;
CC EC=2.7.7.6;
CC -!- SUBUNIT: Component of the RNA polymerase II (Pol II) complex consisting
CC of 12 subunits. {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}.
CC -!- DOMAIN: The C-terminal domain (CTD) serves as a platform for assembly
CC of factors that regulate transcription initiation, elongation,
CC termination and mRNA processing. {ECO:0000305}.
CC -!- PTM: The tandem 7 residues repeats in the C-terminal domain (CTD) can
CC be highly phosphorylated. The phosphorylation activates Pol II.
CC Phosphorylation occurs mainly at residues 'Ser-2' and 'Ser-5' of the
CC heptapeptide repeat. The phosphorylation state is believed to result
CC from the balanced action of site-specific CTD kinases and phosphatase,
CC and a 'CTD code' that specifies the position of Pol II within the
CC transcription cycle has been proposed. {ECO:0000269|PubMed:18257517}.
CC -!- MISCELLANEOUS: The binding of ribonucleoside triphosphate to the RNA
CC polymerase II transcribing complex probably involves a two-step
CC mechanism. The initial binding seems to occur at the entry (E) site and
CC involves a magnesium ion temporarily coordinated by three conserved
CC aspartate residues of the two largest RNA Pol II subunits. The
CC ribonucleoside triphosphate is transferred by a rotation to the
CC nucleotide addition (A) site for pairing with the template DNA. The
CC catalytic A site involves three conserved aspartate residues of the RNA
CC Pol II largest subunit which permanently coordinate a second magnesium
CC ion.
CC -!- SIMILARITY: Belongs to the RNA polymerase beta' chain family.
CC {ECO:0000305}.
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DR EMBL; X56564; CAA39916.1; -; Genomic_DNA.
DR EMBL; CU329671; CAB57941.1; -; Genomic_DNA.
DR PIR; S26849; S26849.
DR RefSeq; NP_595673.1; NM_001021568.2.
DR PDB; 3H0G; X-ray; 3.65 A; A/M=1-1752.
DR PDB; 4PZ6; X-ray; 2.41 A; P/Q=1704-1724.
DR PDB; 5U0S; EM; 7.80 A; a=1-1752.
DR PDBsum; 3H0G; -.
DR PDBsum; 4PZ6; -.
DR PDBsum; 5U0S; -.
DR AlphaFoldDB; P36594; -.
DR SMR; P36594; -.
DR BioGRID; 276823; 166.
DR IntAct; P36594; 9.
DR MINT; P36594; -.
DR STRING; 4896.SPBC28F2.12.1; -.
DR iPTMnet; P36594; -.
DR MaxQB; P36594; -.
DR PaxDb; P36594; -.
DR PRIDE; P36594; -.
DR EnsemblFungi; SPBC28F2.12.1; SPBC28F2.12.1:pep; SPBC28F2.12.
DR GeneID; 2540292; -.
DR KEGG; spo:SPBC28F2.12; -.
DR PomBase; SPBC28F2.12; rpb1.
DR VEuPathDB; FungiDB:SPBC28F2.12; -.
DR eggNOG; KOG0260; Eukaryota.
DR HOGENOM; CLU_000487_3_0_1; -.
DR InParanoid; P36594; -.
DR OMA; SLLHICM; -.
DR PhylomeDB; P36594; -.
DR BRENDA; 2.7.7.6; 5613.
DR Reactome; R-SPO-113418; Formation of the Early Elongation Complex.
DR Reactome; R-SPO-5578749; Transcriptional regulation by small RNAs.
DR Reactome; R-SPO-674695; RNA Polymerase II Pre-transcription Events.
DR Reactome; R-SPO-6781823; Formation of TC-NER Pre-Incision Complex.
DR Reactome; R-SPO-6782135; Dual incision in TC-NER.
DR Reactome; R-SPO-6782210; Gap-filling DNA repair synthesis and ligation in TC-NER.
DR Reactome; R-SPO-6796648; TP53 Regulates Transcription of DNA Repair Genes.
DR Reactome; R-SPO-6807505; RNA polymerase II transcribes snRNA genes.
DR Reactome; R-SPO-72086; mRNA Capping.
DR Reactome; R-SPO-72165; mRNA Splicing - Minor Pathway.
DR Reactome; R-SPO-73776; RNA Polymerase II Promoter Escape.
DR Reactome; R-SPO-73779; RNA Polymerase II Transcription Pre-Initiation And Promoter Opening.
DR Reactome; R-SPO-75953; RNA Polymerase II Transcription Initiation.
DR Reactome; R-SPO-75955; RNA Polymerase II Transcription Elongation.
DR Reactome; R-SPO-76042; RNA Polymerase II Transcription Initiation And Promoter Clearance.
DR Reactome; R-SPO-77075; RNA Pol II CTD phosphorylation and interaction with CE.
DR Reactome; R-SPO-9018519; Estrogen-dependent gene expression.
DR EvolutionaryTrace; P36594; -.
DR PRO; PR:P36594; -.
DR Proteomes; UP000002485; Chromosome II.
DR GO; GO:0000785; C:chromatin; IDA:PomBase.
DR GO; GO:0005829; C:cytosol; HDA:PomBase.
DR GO; GO:0005634; C:nucleus; HDA:PomBase.
DR GO; GO:0005665; C:RNA polymerase II, core complex; IDA:PomBase.
DR GO; GO:0003677; F:DNA binding; IDA:PomBase.
DR GO; GO:0003899; F:DNA-directed 5'-3' RNA polymerase activity; IEA:UniProtKB-EC.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006366; P:transcription by RNA polymerase II; EXP:PomBase.
DR DisProt; DP02514; -.
DR Gene3D; 1.10.132.30; -; 1.
DR Gene3D; 1.10.274.100; -; 1.
DR Gene3D; 3.30.1360.140; -; 1.
DR Gene3D; 4.10.860.120; -; 2.
DR InterPro; IPR045867; DNA-dir_RpoC_beta_prime.
DR InterPro; IPR000722; RNA_pol_asu.
DR InterPro; IPR000684; RNA_pol_II_repeat_euk.
DR InterPro; IPR006592; RNA_pol_N.
DR InterPro; IPR007080; RNA_pol_Rpb1_1.
DR InterPro; IPR007066; RNA_pol_Rpb1_3.
DR InterPro; IPR042102; RNA_pol_Rpb1_3_sf.
DR InterPro; IPR007083; RNA_pol_Rpb1_4.
DR InterPro; IPR007081; RNA_pol_Rpb1_5.
DR InterPro; IPR007075; RNA_pol_Rpb1_6.
DR InterPro; IPR007073; RNA_pol_Rpb1_7.
DR InterPro; IPR038593; RNA_pol_Rpb1_7_sf.
DR InterPro; IPR044893; RNA_pol_Rpb1_clamp_domain.
DR InterPro; IPR038120; Rpb1_funnel_sf.
DR PANTHER; PTHR19376; PTHR19376; 1.
DR Pfam; PF04997; RNA_pol_Rpb1_1; 1.
DR Pfam; PF00623; RNA_pol_Rpb1_2; 1.
DR Pfam; PF04983; RNA_pol_Rpb1_3; 1.
DR Pfam; PF05000; RNA_pol_Rpb1_4; 1.
DR Pfam; PF04998; RNA_pol_Rpb1_5; 1.
DR Pfam; PF04992; RNA_pol_Rpb1_6; 1.
DR Pfam; PF04990; RNA_pol_Rpb1_7; 1.
DR Pfam; PF05001; RNA_pol_Rpb1_R; 19.
DR SMART; SM00663; RPOLA_N; 1.
DR PROSITE; PS00115; RNA_POL_II_REPEAT; 24.
PE 1: Evidence at protein level;
KW 3D-structure; DNA-binding; DNA-directed RNA polymerase; Magnesium;
KW Metal-binding; Nucleotidyltransferase; Nucleus; Phosphoprotein;
KW Reference proteome; Repeat; Transcription; Transferase; Zinc.
FT CHAIN 1..1752
FT /note="DNA-directed RNA polymerase II subunit rpb1"
FT /id="PRO_0000073945"
FT REPEAT 1558..1564
FT /note="1"
FT REPEAT 1578..1584
FT /note="2"
FT REPEAT 1585..1591
FT /note="3"
FT REPEAT 1592..1598
FT /note="4"
FT REPEAT 1599..1605
FT /note="5"
FT REPEAT 1606..1612
FT /note="6; approximate"
FT REPEAT 1613..1619
FT /note="7"
FT REPEAT 1620..1626
FT /note="8"
FT REPEAT 1627..1633
FT /note="9"
FT REPEAT 1634..1640
FT /note="10"
FT REPEAT 1641..1647
FT /note="11"
FT REPEAT 1648..1654
FT /note="12"
FT REPEAT 1655..1661
FT /note="13"
FT REPEAT 1662..1668
FT /note="14"
FT REPEAT 1669..1675
FT /note="15"
FT REPEAT 1676..1682
FT /note="16"
FT REPEAT 1683..1689
FT /note="17"
FT REPEAT 1690..1696
FT /note="18"
FT REPEAT 1697..1703
FT /note="19"
FT REPEAT 1704..1710
FT /note="20"
FT REPEAT 1711..1717
FT /note="21"
FT REPEAT 1718..1724
FT /note="22"
FT REPEAT 1725..1731
FT /note="23"
FT REPEAT 1732..1738
FT /note="24"
FT REPEAT 1739..1745
FT /note="25"
FT REPEAT 1746..1752
FT /note="26"
FT REGION 816..828
FT /note="Bridging helix"
FT REGION 1554..1752
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1558..1752
FT /note="C-terminal domain (CTD); 26 X 7 AA approximate
FT tandem repeats of Y-S-P-[TS]-S-P-S"
FT COMPBIAS 1554..1743
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 69
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 72
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 79
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 82
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 109
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 112
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 150
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 175
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 487
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 487
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /ligand_note="ligand shared with RPB2"
FT /evidence="ECO:0000250"
FT BINDING 489
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 489
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /ligand_note="ligand shared with RPB2"
FT /evidence="ECO:0000250"
FT BINDING 491
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT MOD_RES 1489
FT /note="Phosphoserine"
FT /evidence="ECO:0000269|PubMed:18257517"
FT MOD_RES 1499
FT /note="Phosphoserine"
FT /evidence="ECO:0000269|PubMed:18257517"
FT MOD_RES 1506
FT /note="Phosphoserine"
FT /evidence="ECO:0000269|PubMed:18257517"
FT MOD_RES 1529
FT /note="Phosphoserine"
FT /evidence="ECO:0000269|PubMed:18257517"
FT MOD_RES 1531
FT /note="Phosphotyrosine"
FT /evidence="ECO:0000269|PubMed:18257517"
SQ SEQUENCE 1752 AA; 194163 MW; 15A4F0B59E60E570 CRC64;
MSGIQFSPSS VPLRRVEEVQ FGILSPEEIR SMSVAKIEFP ETMDESGQRP RVGGLLDPRL
GTIDRQFKCQ TCGETMADCP GHFGHIELAK PVFHIGFLSK IKKILECVCW NCGKLKIDSS
NPKFNDTQRY RDPKNRLNAV WNVCKTKMVC DTGLSAGSDN FDLSNPSANM GHGGCGAAQP
TIRKDGLRLW GSWKRGKDES DLPEKRLLSP LEVHTIFTHI SSEDLAHLGL NEQYARPDWM
IITVLPVPPP SVRPSISVDG TSRGEDDLTH KLSDIIKANA NVRRCEQEGA PAHIVSEYEQ
LLQFHVATYM DNEIAGQPQA LQKSGRPLKS IRARLKGKEG RLRGNLMGKR VDFSARTVIT
GDPNLSLDEL GVPRSIAKTL TYPETVTPYN IYQLQELVRN GPDEHPGAKY IIRDTGERID
LRYHKRAGDI PLRYGWRVER HIRDGDVVIF NRQPSLHKMS MMGHRIRVMP YSTFRLNLSV
TSPYNADFDG DEMNMHVPQS EETRAEIQEI TMVPKQIVSP QSNKPVMGIV QDTLAGVRKF
SLRDNFLTRN AVMNIMLWVP DWDGILPPPV ILKPKVLWTG KQILSLIIPK GINLIRDDDK
QSLSNPTDSG MLIENGEIIY GVVDKKTVGA SQGGLVHTIW KEKGPEICKG FFNGIQRVVN
YWLLHNGFSI GIGDTIADAD TMKEVTRTVK EARRQVAECI QDAQHNRLKP EPGMTLRESF
EAKVSRILNQ ARDNAGRSAE HSLKDSNNVK QMVAAGSKGS FINISQMSAC VGQQIVEGKR
IPFGFKYRTL PHFPKDDDSP ESRGFIENSY LRGLTPQEFF FHAMAGREGL IDTAVKTAET
GYIQRRLVKA MEDVMVRYDG TVRNAMGDII QFAYGEDGLD ATLVEYQVFD SLRLSTKQFE
KKYRIDLMED RSLSLYMENS IENDSSVQDL LDEEYTQLVA DRELLCKFIF PKGDARWPLP
VNVQRIIQNA LQIFHLEAKK PTDLLPSDII NGLNELIAKL TIFRGSDRIT RDVQNNATLL
FQILLRSKFA VKRVIMEYRL NKVAFEWIMG EVEARFQQAV VSPGEMVGTL AAQSIGEPAT
QMTLNTFHYA GVSSKNVTLG VPRLKEILNV AKNIKTPSLT IYLMPWIAAN MDLAKNVQTQ
IEHTTLSTVT SATEIHYDPD PQDTVIEEDK DFVEAFFAIP DEEVEENLYK QSPWLLRLEL
DRAKMLDKKL SMSDVAGKIA ESFERDLFTI WSEDNADKLI IRCRIIRDDD RKAEDDDNMI
EEDVFLKTIE GHMLESISLR GVPNITRVYM MEHKIVRQIE DGTFERADEW VLETDGINLT
EAMTVEGVDA TRTYSNSFVE ILQILGIEAT RSALLKELRN VIEFDGSYVN YRHLALLCDV
MTSRGHLMAI TRHGINRAET GALMRCSFEE TVEILMDAAA SGEKDDCKGI SENIMLGQLA
PMGTGAFDIY LDQDMLMNYS LGTAVPTLAG SGMGTSQLPE GAGTPYERSP MVDSGFVGSP
DAAAFSPLVQ GGSEGREGFG DYGLLGAASP YKGVQSPGYT SPFSSAMSPG YGLTSPSYSP
SSPGYSTSPA YMPSSPSYSP TSPSYSPTSP SYSPTSPSYS PTSPSYSATS PSYSPTSPSY
SPTSPSYSPT SPSYSPTSPS YSPTSPSYSP TSPSYSPTSP SYSPTSPSYS PTSPSYSPTS
PSYSPTSPSY SPTSPSYSPT SPSYSPTSPS YSPTSPSYSP TSPSYSPTSP SYSPTSPSYS
PTSPSYSPTS PS
